Protein:CD247 |
Protein Summary |
 Gene summary |
| Gene name: CD247 | ASpdb.0 ID: 919 | Gene | Gene symbol | CD247 | Gene ID | 919 |
| Gene name | CD247 molecule |
| Synonyms | CD3-ZETA|CD3H|CD3Q|CD3Z|CD3ZETA|IMD25|T3Z|TCRZ |
| Cytomap | 1q24.2 |
| Type of gene | protein-coding |
| Description | T-cell surface glycoprotein CD3 zeta chainCD247 antigen, zeta subunitCD3Z antigen, zeta polypeptide (TiT3 complex)CD3zeta chainT-cell antigen receptor complex, zeta subunit of CD3T-cell receptor T3 zeta chainTCR zeta chaintissue factor-targeting CA |
| Modification date | 20240305 |
| UniProtAcc | P20963 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | CD247 | GO:0005737 | cytoplasm | 11390434 |
| Gene | CD247 | GO:0005886 | plasma membrane | 1390434|2532305|11390434|31461748 |
| Gene | CD247 | GO:0033001 | Fc-gamma receptor III complex | 1825220|28652325 |
| Gene | CD247 | GO:0038094 | Fc-gamma receptor signaling pathway | 8478617 |
| Gene | CD247 | GO:0042101 | T cell receptor complex | 8176201 |
| Gene | CD247 | GO:0042105 | alpha-beta T cell receptor complex | 9485181 |
| Gene | CD247 | GO:0042802 | identical protein binding | 14967045 |
| Gene | CD247 | GO:0042803 | protein homodimerization activity | 1825220|2532305|28652325 |
| Gene | CD247 | GO:0046982 | protein heterodimerization activity | 1825220 |
| Gene | CD247 | GO:0065003 | protein-containing complex assembly | 9485181 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P20963-1 | P20963-1_6jxr_a.pdb | 6JXR | EM | 3.7 | a | 22 | 57 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P20963 | CD247 | P20963-1 | P20963-3 | 164 | 163 | 101 | 101 | Deletion | none | none | 100 | 100 |
| Multiple sequence alignment of our canonical and alternatively spliced CD247 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CD247 |
| UniProt-id | ENSG | ENST | ENSP |
| P20963-1 | ENSG00000198821.12 | ENST00000362089.10 | ENSP00000354782.5 |
| P20963-3 | ENSG00000198821.12 | ENST00000392122.4 | ENSP00000375969.3 |
| UniProt-id | NM ID | NP ID |
| P20963-1 | NM_198053.2 | NP_932170.1 |
| P20963-3 | NM_000734.3 | NP_000725.1 |
| Amino acid sequences of our canonical and alternatively spliced CD247 |
| accession_id | Protein sequence |
| P20963-1 | MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRR |
| P20963-3 | MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRR |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| CD247 (go to UniProt):P20963 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P20963 | Topological domain | 52 | 164 | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 | Type=Deletion;Start=101;End=101 |
| P20963 | Domain | 100 | 128 | Note=ITAM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00379 | Type=Deletion;Start=101;End=101 |
| P20963 | Region | 83 | 111 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=101;End=101 |
| P20963 | Compositional bias | 83 | 102 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=101;End=101 |
Gene Isoform Structures and Expression Levels for CD247 |
| Gene structures of our canonical and alternative spliced genes of CD247 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P20963-1 |
| 3D view using mol* of P20963-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P20963-1 |
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| pLDDT distribution across the protein length of P20963-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P20963-1 |
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| Ramachandran plot of P20963-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P20963-1 | 0.703 | 48 | 0.69 | 100.499 | 0.718 | 0.547 | 0.708 | 0.524 | 0.89 | 0.589 | 1.063 | 139,141,142,143,145,147,149,150,153,154,157
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| P20963-3 | 0.559 | 25 | 0.408 | 28.126 | 0.671 | 0.587 | 0.952 | 0.105 | 1.271 | 0.083 | 0.45 | 56,57,60,77,78,79,80,81
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Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P20963-1_P20963-1_6jxr_a.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P20963-1_6jxr_a_P20963-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P20963-1_P20963-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P20963-1_vs_P20963-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P20963-1_vs_P20963-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to CD247 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| P20963 | CD247 | DB00075 | Muromonab | approved, investigational |
Related Diseases to CD247 |
| Previous studies relating to the alternative splicing of CD247 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| CD247 | 20118245 | Alternative splicing factor/splicing factor 2 regulates the expression of the zeta subunit of the human T cell receptor-associated CD3 complex. | "T cells from patients with systemic lupus erythematosus express decreased levels of the T cell receptor-associated CD3 zeta chain, a feature directly linked to their aberrant function. The decrease in CD3zeta protein expression is in part due to decreased levels of functional wild type isoform of the 3'-untranslated region (UTR) of CD3zeta mRNA with concomitant increased levels of an unstable alternatively spliced isoform. In order to identify factors involved in the post-transcriptional regulation of CD3zeta, we performed mass spectrometric analysis of Jurkat T cell nuclear proteins ""pulled down"" by a CD3zeta 3'-UTR oligonucleotide, which identified the splicing protein alternative splicing factor/splicing factor 2 (ASF/SF2). We show for the first time that ASF/SF2 binds specifically to the 3'-UTR of CD3zeta and regulates expression of CD3zeta protein by limiting the production of the alternatively spliced isoform. During activation of human T cells, an increase in the wild type CD3zeta mRNA is associated with increased expression of ASF/SF2. Finally, we show a significant correlation between ASF/SF2 and CD3zeta protein levels in T cells from systemic lupus erythematosus patients. Thus, our results identify ASF/SF2 as a novel factor in the regulation of alternative splicing of the 3'-UTR of CD3zeta and protein expression in human T cells." | D008180 | Lupus Erythematosus, Systemic |
| CD247 | 23228155 | Alternative expression of TCRζ related genes in patients with chronic myeloid leukemia. | A previous study has demonstrated a significant decrease in the TCRζ gene expression level in chronic myeloid leukemia (CML); thus, we further investigated the expression of TCRζ-regulating factors, the distribution of the TCRζ 3' untranslated region (3'-UTR) splice variants, and the expression level and correlation of the alternative splicing factor/splicing factor 2 (ASF/SF-2), FcεRIγ and ZAP-70 genes. TCRζ 3'-UTR splice variants were identified in peripheral blood mononuclear cells (PBMCs) from 14 healthy individuals, 40 patients with CML and 22 patients with CML in complete remission (CML-CR) by RT-PCR. The expression level of the TCRζ, FcεRIγ, ASF/SF-2 and ZAP-70 genes was analyzed by real-time quantitative PCR. While the expression of TCRζ gene in the CML group was significantly lower than that in the healthy individual and CML-CR groups, a significantly higher expression of the FceRIγ and ASF/SF-2 genes was found in the CML group. Two types of splicing forms were detected in all of the healthy individual CML-CR cases: wild type (WT) TCRζ 3'-UTR and alternatively splieced (AS) TCRζ 3'-UTR which have been alternatively splieced in the WT TCRζ 3'-UTR . However, 35% of the CML cases contained only the wild type TCRζ 3'-UTR isoform. Based on the TCRζ 3'-UTR isoform expression characteristic, we divided the patients with CML into two subgroups: the WT+AS- CML group, containing patients that express only the wild type TCRζ 3'-UTR, and the WT+AS+ CML group, which contained patients that expressed two TCRζ 3'-UTR isoforms. A significantly different ASF/SF-2 and FcεRIγ gene expression pattern was found between the WT+AS- and WT+AS+CML groups. We concluded that defective TCRζ expression may be characterized in the WT+AS-and WT+AS+CML subgroups by the different gene expression pattern. The overexpression of ASF/SF2, which alternatively splices the TCRζ 3'-UTR, is thought to participate in feedback regulation. The characteristics of TCRζ 3'-UTR alternative splicing may be a novel immunological marker for the evaluation of the CML immune status. | D015464 | Leukemia, Myelogenous, Chronic, BCR-ABL Positive |
Clinically important variants in CD247 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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